4I75

Crystal structure of the Trypanosoma brucei Inosine-Adenosine-Guanosine nucleoside hydrolase in complex with the NiTris metalorganic complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I71TbbIAGNH-363 complex

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.62920.1M Tris, 23% PEGMME2000, 10mM Ni2SO4, pH 8.6, VAPOR DIFFUSION, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.0138.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.7α = 90
b = 134.89β = 90
c = 60.99γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87260ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.86899.40.06814.293.75444254442-325.787
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8594.70.5610.662.63.53780

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTTbbIAGNH-363 complex1.848.85444254442276199.40.18250.18040.2232RANDOM20.222
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.74-0.960.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.025
r_dihedral_angle_4_deg17.141
r_dihedral_angle_3_deg15.04
r_sphericity_free14.508
r_dihedral_angle_1_deg6.243
r_scangle_it3.979
r_scbond_it2.577
r_angle_refined_deg1.608
r_mcangle_it1.437
r_angle_other_deg1.164
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.025
r_dihedral_angle_4_deg17.141
r_dihedral_angle_3_deg15.04
r_sphericity_free14.508
r_dihedral_angle_1_deg6.243
r_scangle_it3.979
r_scbond_it2.577
r_angle_refined_deg1.608
r_mcangle_it1.437
r_angle_other_deg1.164
r_mcbond_it0.807
r_mcbond_other0.272
r_chiral_restr0.101
r_bond_refined_d0.019
r_bond_other_d0.004
r_gen_planes_refined0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4972
Nucleic Acid Atoms
Solvent Atoms492
Heterogen Atoms51

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction